This function takes a region annotation object and reads in the regions, returning a GRangesList object of the regions.

This function takes a region annotation object and reads in the regions, returning a GRangesList object of the regions.

readRegionGRL(dbLocation, annoDT, refreshCaches = FALSE, useCache = TRUE,
  limit = NULL)

Arguments

dbLocation

folder of regiondB
annoDT

output of readRegionSetAnnotation().
refreshCaches

should I recreate the caches?
useCache

uses simpleCache to cache and load the results
limit

for testing purposes, limit the nmber of files read. NULL for no limit (default).

Value

GRangesList object

Examples

dbPath = system.file("extdata", "hg19", package="LOLA")
regionAnno = readRegionSetAnnotation(dbLocation=dbPath)
#> Reading region annotations...
#> ::Loading cache::	/sfs/lustre/scratch/ns5bc/code/LOLA/inst/extdata/hg19/ucsc_example//ucsc_example_files.RData
regionGRL = readRegionGRL(dbLocation= dbPath, regionAnno, useCache=FALSE)
#> ucsc_example
#> Reading 5 files...
#> 1: /sfs/lustre/scratch/ns5bc/code/LOLA/inst/extdata/hg19/ucsc_example/regions/cpgIslandExt.bed
#> 2: /sfs/lustre/scratch/ns5bc/code/LOLA/inst/extdata/hg19/ucsc_example/regions/laminB1Lads.bed
#> 3: /sfs/lustre/scratch/ns5bc/code/LOLA/inst/extdata/hg19/ucsc_example/regions/numtSAssembled.bed
#> 4: /sfs/lustre/scratch/ns5bc/code/LOLA/inst/extdata/hg19/ucsc_example/regions/vistaEnhancers.bed
#> 5: /sfs/lustre/scratch/ns5bc/code/LOLA/inst/extdata/hg19/ucsc_example/regions/vistaEnhancers_colNames.bed